polyphys 1.0.0__py3-none-any.whl

polyphys/tests/data/lammps_build/make_starts.py

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+"""Write the start configurations that ``in.kg`` checks.
+
+Run from the project environment::
+
+    python make_starts.py OUTDIR
+
+It writes, with :mod:`polyphys.simulate.build`, ``helix.data`` (a linear
+helix of 200 beads, radius 2, pitch 2.5, atom style ``bond``),
+``ring.data`` (a plectoneme ring of 200 beads, the same radius and pitch,
+atom style ``bond``), and ``ring_angle.data`` (the same ring with angles,
+atom style ``angle``), each in a box that is periodic along z only and wide
+enough for a cylinder of diameter 5.2 about the z axis, and prints the
+:func:`~polyphys.simulate.build.check_conformation` report of each. The
+same configurations are built by ``test_build.py``; this script is for a
+run by hand with ``check_starts.sh``.
+"""
+
+import sys
+from pathlib import Path
+
+import numpy as np
+
+from polyphys.simulate.build import (
+    chain_data,
+    check_conformation,
+    helix,
+    plectoneme_ring,
+)
+from polyphys.simulate.core import Box
+from polyphys.simulate.data import write_data
+
+N_BEADS = 200
+RADIUS = 2.0
+PITCH = 2.5
+HALF_WIDTH = 5.0        # x and y half-width of the box; the wall at 3.1 fits
+MARGIN = 2.0            # z margin on each side, beyond the ghost cutoff
+GHOST_CUTOFF = 1.122462 + 0.3
+PERIODIC = (False, False, True)
+
+
+def start_box(positions: np.ndarray) -> Box:
+    """Return a box of the configuration's height plus the margins."""
+    half_height = 0.5 * float(np.ptp(positions[:, 2])) + MARGIN
+    return Box(lo=np.array([-HALF_WIDTH, -HALF_WIDTH, -half_height]),
+               hi=np.array([HALF_WIDTH, HALF_WIDTH, half_height]))
+
+
+def main(out_dir: Path) -> None:
+    out_dir.mkdir(parents=True, exist_ok=True)
+    line = helix(N_BEADS, radius=RADIUS, pitch=PITCH)
+    ring = plectoneme_ring(N_BEADS, radius=RADIUS, pitch=PITCH)
+    files = {
+        "helix.data": chain_data(line, start_box(line)),
+        "ring.data": chain_data(ring, start_box(ring), ring=True),
+        "ring_angle.data": chain_data(ring, start_box(ring), ring=True,
+                                      angles=True),
+    }
+    for name, data in files.items():
+        cylinder = {"dcyl": 5.2, "dmon": 1.0} if name == "helix.data" else {}
+        report = check_conformation(data, r0=1.5, ghost_cutoff=GHOST_CUTOFF,
+                                    periodic=PERIODIC, **cylinder)
+        path = write_data(data, out_dir / name,
+                          title=f"{name}: polyphys.simulate.build start")
+        print(f"{path.name}: {report}")
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 2:
+        sys.exit("usage: python make_starts.py OUTDIR")
+    main(Path(sys.argv[1]))